Introduction

immunarch is an R package designed to analyse TCR and BCR (immunoglobulin) repertoires, which constitute a large amount of data. The mission of immunarch is to make immune sequencing data analysis as effortless as possible—and help you focus on research instead of coding.

Features

Fast and easy manipulation of immune repertoire data:

The package automatically detects the format of your files—no more guessing what format is that file, just pass them to the package;

Supports all popular TCR and BCR analysis and post-analysis formats: ImmunoSEQ, IMGT, MiTCR, MiXCR, MiGEC, MigMap, VDJtools, tcR. More coming in the future;

After downloading the file, you need to install a number of packages with R commands listed below, and run the newly installed devtools package to install immunarch locally. Upon completion the dependencies will have been already downloaded and installed.

Installation troubleshooting

Check your R version. Run version command in the console to get your R versions. If the R version is below 3.4.0 (for example, R version 3.1.0), try updating your R version to the latest one.

Check if your packages are outdated and update them. In RStudio you can run the “Update” button on top of the package list. In R console you can run the old.packages() command to view a list of outdated packages.

If you are on Mac and have issues like old packages can’t be updated, or error messages such as ld: warning: directory not found for option or ld: library not found for -lgfortran, this link will help you to fix the issue.

If you are working under Linux and have issues with igraph library or have Fortran errors, see this link